AMBER Archive (2003)

Subject: Re: Minimization problem w/ counter-ion !

From: David A. Case (case_at_scripps.edu)
Date: Thu May 22 2003 - 11:51:28 CDT

On Thu, Oct 31, 2002, Marco Preto wrote:
>
> I'm trying to run a minimization of a solvent box (with my solute and
> Cl- fixed) to get a better starting point to the equilibration dynamic
> run of my system. Unfortunatly I'm having trouble with the electrostatic
> interactions (this value goes to so negative magnitude that the format
> is not suficient to writ it and my output comes like ***********. I've
> tryed to put the counter ion using addions and when that did not work I
> tryed to put it manually on my system, in diferent positions, but the
> calculations allways stoped with a segmentation fault, during this
> minimization.
>
> &cntrl
> imin=1, maxcyc=200000, cut=12, igb=0,
> ntb=1, ntpr=1000, ncyc=2000,
> ibelly=1, ntwx=100,
> &end
> Group input for moving atoms
> RES 10 3846
> END
> END
>
>
> Res 10 to 3846 are my water molecules!

The problem most likely is that you are not using SHAKE for your waters; you
*must* set ntc=ntf=2 to use the TIP3P water model, otherwise you will get
exactly the behavior you describe: the O-H bonds in the water can stretch, and
lead to "fusion" betwee the hydrogens (which have no vdW radii in this model)
and other charges (like those of the counterions.)

Second, why are you running 200000 steps of minimization? I'd suggest a value
somewhere between two and three orders of magnitude smaller.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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